9NWN | pdb_00009nwn

Structure of minimal CRISPR polymerase bound to ApNHpp

• PDB DOI: https://doi.org/10.2210/pdb9NWN/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2025-03-24 Released: 2025-08-27 
• Deposition Author(s): Doherty, E.E., Bolling, C.B., Wilcox, X.E., Doudna, J.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: in silico

Literature

A miniature CRISPR-Cas10 enzyme confers immunity by inhibitory signalling.

Doherty, E.E., Adler, B.A., Yoon, P.H., Hsieh, K., Loi, K., Armbruster, E.G., Lahiri, A., Bolling, C.S., Wilcox, X.E., Akkati, A., Iavarone, A.T., Pogliano, J., Doudna, J.A.

(2025) Nature 647: 997-1004

• PubMed: 41034576 
• DOI: https://doi.org/10.1038/s41586-025-09569-9
• Primary Citation Related Structures: 
  9NWN


• PubMed Abstract: 
  

  Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signalling that share mechanistic features with human antiviral systems ¹ . In these pathways, including cyclic oligonucleotide-based antiphage signalling systems (CBASSs) and type III CRISPR systems in bacteria and cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response ^2-4 . Here, in an unexpected inversion of this process, we show that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that represses a toxic effector. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful defence strategy against virus-mediated immune suppression, expanding our understanding of the role of oligonucleotides in immunity.

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Organizational Affiliation: 
• Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA.
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.15 kDa 
• Atom Count: 2,032 
• Modeled Residue Count: 240 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MCpol domain-containing protein	A [auth B], B [auth A]	125	Escherichia coli	Mutation(s): 0  Gene Names: DU321_04150
UniProt
Find proteins for A0A426EXS8 (Escherichia coli) Explore A0A426EXS8  Go to UniProtKB:  A0A426EXS8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZAN (Subject of Investigation/LOI)	C [auth B], E [auth A]	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine C10 H17 N6 O12 P3 WUPFAKUEHUVIDK-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	D [auth B], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.135	α = 90
b = 56.769	β = 90
c = 93.705	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Doherty, E.E., Bolling, C.B., Wilcox, X.E., Doudna, J.A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM153031

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2026-03-11
  Changes: Database references